I'm using the release you have posted on the releases page on your github.
It looks like the problem isn't even the related cIOS, it's just not reloading into it with your fork, even if I stick the exact same IOS in slot 250 as 249.
On top of this, on my console if I set the Loader IOS to be something different from the Game IOS, it fails to load any game.
For example, if I set loader IOS to 58, and set Game IOS to the usual 249, restart the loader, and try to play anything, it will just kick me to homebrew channel.
To me that says it's having a hard time performing reloads into other IOSs
Also, why don't you want to support beta53-alt anyway? It's extremely commonly used.
Almost every guide out there has people using it, and I've never experienced any issues. The D2X-wiki says it's identical to 52 but with Plug-n-play USB support at the expense of improved emunand support- which for games like Just Dance, Guitar Hero, and Rock Band is pretty useful.